Add test yml files

[SusiJo]

Many thanks to contributing to nf-core/bamtofastq!

PR checklist

• [x] This comment contains a description of changes (with reason)
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If necessary, add test data to testdata/
• [x] Ensure the test suite passes (nextflow run . -profile test,docker).
• [x] Make sure your code lints (nf-core lint .).
• [x] Documentation in docs is updated
• [x] CHANGELOG.md is updated
• [x] README.md is updated

Learn more about contributing: https://github.com/qbic-pipelines/bamtofastq/tree/master/.github/CONTRIBUTING.md

[maxulysse]

Looking good. Only issue I see, is that test data appears not to be in https://github.com/nf-core/test-datasets

[SusiJo]

Should I copy the nf-core testdata that I used for the pipeline to the bamtofastq branch?

[maxulysse]

@SusiJo you still need to include the params you add in the test profile in the other profiles. The way we do it in sarek, is simply by doing -profile test,<other_test_profile>

[SusiJo]

@maxulysse since I removed the { includeConfig 'conf/test.config' } from the other test_profiles (test_chr.config , ...) it's not loading the maximal resource requirements from the test.config anymore and uses the base.config instead. Therefore the GHA are not running anymore. How can I still load the test.config for all the tests? I was following the sarek way of configuration, but it's not working. Am I missing something?

[maxulysse]

@maxulysse since I removed the { includeConfig 'conf/test.config' } from the other test_profiles (test_chr.config , ...) it's not loading the maximal resource requirements from the test.config anymore and uses the base.config instead. Therefore the GHA are not running anymore. How can I still load the test.config for all the tests? I was following the sarek way of configuration, but it's not working. Am I missing something?

The way we do it in sarek, is simply by doing -profile test,

What can probably try, is include both files in profiles